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Full Discussion: Help with shell script - not finding files
Top Forums Shell Programming and Scripting Help with shell script - not finding files Post 302873259 by wmelroy on Monday 11th of November 2013 01:56:20 PM
Old 11-11-2013
Help with shell script - not finding files
Hello,

I have a shell script like the one below but cannot get it working:
Code:
#!/bin/bash
#$ -cwd

CHR=$2
 
# directories
ROOT_DIR=./
RESULTS_DIR=${ROOT_DIR}results/
 
# executable
SHAPEIT_EXEC=${ROOT_DIR}shapeit.v2.r727.linux.x64/shapeit.v2.r727.linux.x64
 
# parameters
THREAT=5
EFFECTIVESIZE=11418
 
# reference data files
GENMAP_FILE=/home/whme1016/Imputation/genetic_map_b37/genetic_map_chr${CHR}_combined_b37.txt
 
# GWAS data files in PLINK BED format
GWASDATA_BED=${ROOT_DIR}chr${CHR}.unphased.bed
GWASDATA_BIM=${ROOT_DIR}chr${CHR}.unphased.bim
GWASDATA_FAM=${ROOT_DIR}chr${CHR}.unphased.fam

# problem SNP file
EXCLUDE_SNP=${ROOT_DIR}chr${CHR}.alignments.snp.strand.exclude
 
# main output file
OUTPUT_HAPS=${RESULTS_DIR}chr${CHR}.phased.haps
OUTPUT_SAMPLE=${RESULTS_DIR}chr${CHR}.phased.sample
OUTPUT_LOG=${RESULTS_DIR}chr${CHR}.phased.log
 
## phase GWAS genotypes
$SHAPEIT_EXEC \
--input-bed $GWASDATA_BED $GWASDATA_BIM $GWASDATA_FAM \
--input-map $GENMAP_FILE \
--exclude-snp $EXCLUDE_SNP \
--thread $THREAT \
--effective-size $EFFECTIVESIZE \
--output-max $OUTPUT_HAPS $OUTPUT_SAMPLE \
--output-log $OUTPUT_LOG

done

I am trying to run a program called SHAPEIT. When I run the shell script, I get the following error:
Code:
Segmented HAPlotype Estimation & Imputation Tool
  * Authors : Joe BLOGGS
  * Contact : someone@somewhere.com
  * Webpage : http:://www.example.fr
  * Version : v2.r727
ERROR: [./chr.alignments.snp.strand.exclude] is impossible to open, check file existence or reading permissions

I have the following files in my root directory for chromosome 2 with full permissions:
Code:
chr2.alignments.log                 
chr2.alignments.snp.strand        
chr2.alignments.snp.strand.exclude 
chr2.unphased.bed                   
chr2.unphased.bim                   
chr2.unphased.fam                   
chr2.unphased.log

My shell script is clearly reading the chr2.unphased.fam/bed/bim files, but not my chr2.alignments.snp.strand.exclude. Any ideas why this is? Thanks for any help.
Last edited by Scott; 11-11-2013 at 02:58 PM.. Reason: Add code tags; obfuscate data
 

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LEARN ABOUT LINUX

snp

SNP(4)                                                     BSD Kernel Interfaces Manual                                                     SNP(4)

NAME

     snp -- tty snoop interface

SYNOPSIS

     #include <sys/snoop.h>

     int
     ioctl(fd, SNPSTTY, &dev);

     int
     ioctl(fd, SNPGTTY, &dev);

     int
     ioctl(fd, FIONREAD, &result);

DESCRIPTION

     /dev/snp is a snoop device which allows users to attach to any tty and watch activities on it.  The kernel must be compiled with device snp,
     or the snp module must be loaded, for these devices to be available.

     To associate a given snp device with a tty to be observed, open the snp device and a tty device, and then issue the SNPSTTY ioctl on snp
     device.  The argument passed to the ioctl(2) is the address of a variable of type int, holding the file descriptor of a tty device.  To
     detach the snp device from a tty use a pointer to a value of -1.

     The SNPGTTY ioctl returns information about the current tty attached to the open snp device.

     The FIONREAD ioctl returns a positive value equal to the number of characters in a read buffer.  Special values defined are:

     SNP_OFLOW     device overflow occurred, device detached.

     SNP_TTYCLOSE  tty not attached.

     SNP_DETACH    snp device has been detached by user or tty device has been closed and detached.

SEE ALSO

     pty(4), sio(4), kldload(8), watch(8)

HISTORY

     The snp device first appeared in FreeBSD 2.1.  In FreeBSD 8.0 the snp driver was rewritten to work with the replaced TTY subsystem.

AUTHORS

     The author of the current implementation is Ed Schouten <ed@FreeBSD.org>.  Previous versions of snp were based on code written by
     Ugen J.S. Antsilevich <ugen@NetVision.net.il>.

BUGS

     This version of snp does not return proper error codes when calling FIONREAD.  It also does not allow SNPSTTY to detach itself from the TTY.

BSD                                                              November 5, 2008                                                              BSD
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